org.bridgedb.tools.qc

Class BridgeQC

java.lang.Object

org.bridgedb.tools.qc.BridgeQC

public class BridgeQC
extends Object

Utility to do simple quality control on a BridgeDerby database. Run with two parameters: [old database] and [new database] Some basic comparisons will be done, which serves as a sanity check that not suddenly a whole identifier system has gone missing.

The script produces a report on STDOUT (configurable), lines starting with "INFO" are strictly informative, whereas lines starting with "WARNING" are problems worth investigating further. Ideally there are no "WARNING" lines in the report.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	BridgeQC.PropertyChecker

Constructor Summary

Constructors

Constructor and Description
BridgeQC(File f1, File f2) Compares two Derby databases and reports the output to STDOUT.
BridgeQC(File f1, File f2, OutputStream out) Compares two Derby databases and reports the output to the given OutputStream.

Method Summary

Modifier and Type	Method and Description
void	checkDatabaseSanity()
void	compareAttributes()
void	compareDataSources()
void	compareFileSizes()
void	compareInfo()
void	compareLinks()
void	initDatabases()
static void	main(String[] args)
static void	printUsage()
void	run()
static boolean	safeEquals(Object a, Object b)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BridgeQC

public BridgeQC(File f1,
                File f2)
         throws IDMapperException

Compares two Derby databases and reports the output to STDOUT.

Parameters:

f1 - the original Derby@prefix gpml: . database

f2 - the new Derby database

Throws:

IDMapperException

BridgeQC

public BridgeQC(File f1,
                File f2,
                OutputStream out)
         throws IDMapperException

Compares two Derby databases and reports the output to the given OutputStream.

Parameters:

f1 - the original Derby database

f2 - the new Derby database

Throws:

IDMapperException

Method Detail

initDatabases

public void initDatabases()
                   throws IDMapperException

Throws:

IDMapperException

compareDataSources

public void compareDataSources()
                        throws IDMapperException

Throws:

IDMapperException

compareLinks

public void compareLinks()
                  throws SQLException

Throws:

SQLException

checkDatabaseSanity

public void checkDatabaseSanity()
                         throws SQLException

Throws:

SQLException

compareFileSizes

public void compareFileSizes()
                      throws SQLException

Throws:

SQLException

compareAttributes

public void compareAttributes()
                       throws IDMapperException

Throws:

IDMapperException

safeEquals

public static boolean safeEquals(Object a,
                                 Object b)

compareInfo

public void compareInfo()

run

public void run()
         throws IDMapperException,
                SQLException

Throws:

IDMapperException

SQLException

printUsage

public static void printUsage()

main

public static void main(String[] args)
                 throws IDMapperException,
                        SQLException

Parameters:

args -

Throws:

IDMapperException

SQLException